Ligand profile

53J

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: KP13_01960 — Dihydrofolate reductase

Via homolog PDB 4elh UniProt Q81R22 Formula C₂₈H₃₀N₆O₃
Mol. weight 498.59 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
53J
PDB
4elh
UniProt (similar protein)
Q81R22
Target protein
KP13_01960

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 498.59 Da
LogP (Crippen) 4.15
H-bond donors 2
H-bond acceptors 8
TPSA 128.95 Ų
Rotatable bonds 7
Aromatic rings 3 / 4
Heavy atoms 37
Fraction sp³ C 0.21
Formula C₂₈H₃₀N₆O₃

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 129.0
  • −1 ≤ LogP ≤ 5 4.15
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 498.6
  • LogP ≤ 5 4.15
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 129.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=C[C@H]1c2ccccc2C=NN1C(=O)/C=C/c3cc(cc(c3OC)OC)Cc4cnc(nc4N)N)C
InChI 
InChI=1S/C28H30N6O3/c1-17(2)11-23-22-8-6-5-7-20(22)16-32-34(23)25(35)10-9-19-12-18(14-24(36-3)26(19)37-4)13-21-15-31-28(30)33-27(21)29/h5-12,14-16,23H,13H2,1-4H3,(H4,29,30,31,33)/b10-9+/t23-/m0/s1
InChIKey 
LEKSMFBSZBQJBZ-ZUTVHTERSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00186

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_01960.

PDB 33

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 100

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)